Dramatic amplification of a rice transposable element during recent domestication
- Ken Naito*,†,
- Eunyoung Cho*,
- Guojun Yang*,
- Matthew A Campbell*,
- Kentaro Yano†,
- Yutaka Okumoto†,
- Takatoshi Tanisaka†, and
- Susan R. Wessler*,‡
- *Department of Plant Biology, University of Georgia, Athens, GA 30602; and
- †Division of Agronomy and Horticulture Science, Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
-
Edited by Vicki L. Chandler, University of Arizona, Tucson, AZ, and approved August 8, 2006 (received for review June 28, 2006)
-
Fig. 1.Copy-number estimation of mPing elements in rice strains. (A) DNA blot of rice genomic DNAs digested with EcoRI and probed with digoxygenin-labeled mPing from the following strains: 1, Nipponbare; 2, Gimbozu EG4; 3, IM294 (irradiated mutant of EG4); 4, Kasalath (indica); 5, A126; 6, A127; 7, A135; 8, A161; 9, A183; 10, G193, 11, A103; 12, A105, 13, A106; 14, G172; 15, G175; 16, A176; 17, A101; 18, A102; 19, A104; 20, G185; 21, G190; 22, G174; 23, A157; 24, A119; 25, A123. Strains named with A are Aikoku-landraces and with G are Gimbozu-landraces. (B) Autoradiograph of a transposon display gel of mPing amplicons in Aikoku and Gimbozu strains. Each DNA sample was digested with MseI, ligated to an adapter, and used as template for PCR with an mPing primer and an adapter primer containing one (+G) selective base. Lane labels refer to the numbers in A and asterisks in A and B indicate the high-copy-number strains. (C) Copy-number estimates derived from transposon display gels. See Results for details.
-
Fig. 2.Target-site preference of mPing insertions. A pictogram was constructed by using the nine nucleotides from 123 insertion sites. In this representation, the size of the letter is proportional to its frequency at a given position (generated at http://genes.mit.edu/pictogram.html by using default parameters). The gray rectangle indicates the trinucleotide duplicated upon insertion.
-
Fig. 3.mPing insertions in or near rice genes. mPing insertions are represented as black triangles, and exons and UTRs are gray and white boxes, respectively, that are connected by introns. Black arrowheads under the boxes represent the positions of primers used for PCR in (Fig. 4)
-
Fig. 4.Analysis of transcription from mPing-containing rice genes. (A) RT-PCR products resolved on agarose gels. Lane numbers refer to genes 1–13 in Fig. 3, where the position of PCR primers is shown for each, whereas M is a 100-base ladder. The source of leaf RNA was Nipponbare (N) or Gimbozu EG4 (G). (B) PCR with genomic DNA from Nipponbare (N) or Gimbozu EG4 (G) using the same primer sets as in A.
-
Fig. 5.Transposon display analysis of mPing insertions of generational material from strain EG4. See Results for details.
Footnotes
- ‡To whom correspondence should be addressed. E-mail: sue{at}plantbio.uga.edu
- © 2006 by The National Academy of Sciences of the USA
